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- PDB-6gxh: The hit-and-return system enables efficient time-resolved serial ... -

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Basic information

Entry
Database: PDB / ID: 6gxh
TitleThe hit-and-return system enables efficient time-resolved serial synchrotron crystallography: FAcD 0MS after reaction initiation
ComponentsFluoroacetate dehalogenase
KeywordsHYDROLASE / time-resolved crystallography / serial synchrotron crystallography (SSX) / Pump-probe experiment / structural enzymology
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsSchulz, E.C. / Mehrabi, P. / Mueller-Werkmeister, H. / Tellkamp, F. / Stuart, W. / Persch, E. / De Gasparo, R. / Diederich, F. / Pai, E.F. / Miller, R.J.D.
CitationJournal: Nat. Methods / Year: 2018
Title: The hit-and-return system enables efficient time-resolved serial synchrotron crystallography.
Authors: Schulz, E.C. / Mehrabi, P. / Muller-Werkmeister, H.M. / Tellkamp, F. / Jha, A. / Stuart, W. / Persch, E. / De Gasparo, R. / Diederich, F. / Pai, E.F. / Miller, R.J.D.
History
DepositionJun 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct_keywords
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase


Theoretical massNumber of molelcules
Total (without water)68,1472
Polymers68,1472
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-18 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.040, 79.970, 84.790
Angle α, β, γ (deg.)90.00, 102.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fluoroacetate dehalogenase


Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG 3350 18 - 20 % CaCl 200 mM TrisHCL 100 mM pH 8.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.96269 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96269 Å / Relative weight: 1
ReflectionResolution: 1.8→86.13 Å / Num. obs: 50502 / % possible obs: 99.9 % / Redundancy: 132.2 % / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSnXDSdata reduction
XSCALEnXSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r3u

3r3u


Resolution: 1.802→57.469 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 5.06 / Phase error: 22.6
RfactorNum. reflection% reflection
Rfree0.2359 2561 5.08 %
Rwork0.1874 --
obs0.1898 50455 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.802→57.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4685 0 0 261 4946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074879
X-RAY DIFFRACTIONf_angle_d0.8646650
X-RAY DIFFRACTIONf_dihedral_angle_d15.0583941
X-RAY DIFFRACTIONf_chiral_restr0.05682
X-RAY DIFFRACTIONf_plane_restr0.006874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8016-1.83630.32921240.28122584X-RAY DIFFRACTION95
1.8363-1.87370.32521370.24612615X-RAY DIFFRACTION100
1.8737-1.91450.25041490.2112683X-RAY DIFFRACTION100
1.9145-1.9590.21661370.19822603X-RAY DIFFRACTION100
1.959-2.0080.26951280.19822697X-RAY DIFFRACTION100
2.008-2.06230.25061180.19422691X-RAY DIFFRACTION100
2.0623-2.1230.25361270.20252645X-RAY DIFFRACTION100
2.123-2.19150.26561560.19642651X-RAY DIFFRACTION100
2.1915-2.26990.25021350.19182652X-RAY DIFFRACTION100
2.2699-2.36070.24731550.18382680X-RAY DIFFRACTION100
2.3607-2.46820.22051690.17592635X-RAY DIFFRACTION100
2.4682-2.59830.21041390.17662658X-RAY DIFFRACTION100
2.5983-2.76110.24551880.18352625X-RAY DIFFRACTION100
2.7611-2.97430.23571350.18182678X-RAY DIFFRACTION100
2.9743-3.27360.22051430.17482669X-RAY DIFFRACTION100
3.2736-3.74720.21231430.1662692X-RAY DIFFRACTION100
3.7472-4.72070.20561620.17432673X-RAY DIFFRACTION100
4.7207-57.49840.26421160.20342763X-RAY DIFFRACTION100

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